Variant report

Variant	rs563385335
Chromosome Location	chr12:49931539-49931540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49931440-49932126	H1-neurons	neurons:	n/a	n/a
2	ZNF263	chr12:49931322-49931852	HEK293-T-REx	kidney:	n/a	chr12:49931744-49931753
3	MAX	chr12:49931520-49933106	A549	lung:	n/a	chr12:49932763-49932772 chr12:49932471-49932480
4	SUZ12	chr12:49931448-49932210	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49931501-49931551	HepG2	liver:	n/a
2	chr12:49931501-49931551	GM12892	blood:	n/a
3	chr12:49931501-49931551	Caco-2	colon:	n/a
4	chr12:49931501-49931551	U87	brain:	n/a
5	chr12:49931501-49931551	HRCEpiC	kidney:	n/a
6	chr12:49931501-49931551	NHBE	bronchial:	n/a
7	chr12:49931501-49931551	BJ	skin:	n/a
8	chr12:49931501-49931551	ProgFib	skin:	n/a
9	chr12:49931501-49931551	HCM	heart:	n/a
10	chr12:49931501-49931551	H1-hESC	embryonic stem cell:	embryo
11	chr12:49931501-49931551	HL-60	blood:	n/a
12	chr12:49931501-49931551	GM19239	blood:	n/a
13	chr12:49931501-49931551	CMK	blood:	n/a
14	chr12:49931501-49931551	GM06990	blood:	n/a
15	chr12:49931501-49931551	AG09319	gingival:	n/a
16	chr12:49931501-49931551	AoSMC	blood vessel:	n/a
17	chr12:49931501-49931551	SKMC	muscle:	n/a
18	chr12:49931501-49931551	HAEpiC	amniotic membrane:	n/a
19	chr12:49931501-49931551	SK-N-SH	brain:	n/a
20	chr12:49931501-49931551	HEEpiC	esophagus:	n/a
21	chr12:49931501-49931551	AG10803	skin:	n/a
22	chr12:49931501-49931551	GM12878	blood:	n/a
23	chr12:49931501-49931551	SK-N-SH_RA	brain:	n/a
24	chr12:49931501-49931551	NT2-D1	testis:	n/a
25	chr12:49931501-49931551	AG09309	skin:	n/a
26	chr12:49931501-49931551	HIPEpiC	eye:	n/a
27	chr12:49931501-49931551	GM12891	blood:	n/a
28	chr12:49931501-49931551	Hepatocyte	liver:	n/a
29	chr12:49931501-49931551	HPAEpiC	pulmonary alveolar:	n/a
30	chr12:49931501-49931551	HCPEpiC	choroid plexus:	n/a
31	chr12:49931501-49931551	SK-N-MC	brain:	n/a
32	chr12:49931501-49931551	K562	blood:	n/a
33	chr12:49931501-49931551	RPTEC	kidney:	n/a
34	chr12:49931501-49931551	ovcar-3	ovarian:	n/a
35	chr12:49931501-49931551	NH-A	brain:	n/a
36	chr12:49931501-49931551	AG04450	lung:	fetal
37	chr12:49931501-49931551	HNPCEpiC	eye:	n/a
38	chr12:49931501-49931551	BE2_C	brain:	n/a
39	chr12:49931501-49931551	HCT-116	colon:	n/a
40	chr12:49931501-49931551	MCF-7	breast:	n/a
41	chr12:49931501-49931551	HUVEC	blood vessel:	n/a
42	chr12:49931501-49931551	T-47D	breast:	n/a
43	chr12:49931501-49931551	LNCaP	prostate:	n/a
44	chr12:49931501-49931551	A549	lung:	n/a
45	chr12:49931501-49931551	SAEC	small airway:	n/a
46	chr12:49931501-49931551	HCF	heart:	n/a
47	chr12:49931501-49931551	PANC-1	pancreas:	n/a
48	chr12:49931501-49931551	ECC-1	luminal epithelium:	n/a
49	chr12:49931501-49931551	AG04449	skin:	fetal
50	chr12:49931501-49931551	IMR90	lung:	fetal

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49930852..49937653-chr12:49953841..49959391,7	K562	blood:
2	chr12:49668500..49671128-chr12:49928861..49931681,2	MCF-7	breast:
3	chr12:49759022..49764027-chr12:49928293..49932911,8	MCF-7	breast:
4	chr12:49759326..49761606-chr12:49928836..49931818,3	MCF-7	breast:
5	chr12:49657477..49660356-chr12:49930384..49933439,3	K562	blood:
6	chr12:49759353..49762276-chr12:49930939..49933731,4	K562	blood:
7	chr12:49930865..49935032-chr12:49959689..49963246,5	K562	blood:
8	chr12:49931420..49936579-chr12:49960006..49963071,6	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNH3-2	chr12:49931398-49931555	NONHSAT028109

No data

Variant related genes	Relation type
KCNH3	TF binding region
KCNH3	CpG island
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3431223	chr12:49931235-49934833	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49929600-49931600	Enhancers	HMEC	breast
2	chr12:49929600-49931600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:49931000-49932400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
4	chr12:49931200-49931600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49931200-49931600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
6	chr12:49931200-49931600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
7	chr12:49931200-49931600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
8	chr12:49931200-49931600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr12:49931200-49931600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:49931200-49931600	Enhancers	Liver	Liver
11	chr12:49931200-49931600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:49931200-49931600	Bivalent Enhancer	HSMM	muscle
13	chr12:49931200-49931600	Bivalent Enhancer	NH-A	brain
14	chr12:49931200-49931800	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr12:49931200-49931800	Flanking Bivalent TSS/Enh	K562	blood
16	chr12:49931200-49932000	Bivalent Enhancer	Fetal Thymus	thymus
17	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
19	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
21	chr12:49931200-49932400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chr12:49931200-49932400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
26	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr12:49931200-49932400	Flanking Active TSS	Right Ventricle	heart
28	chr12:49931200-49932400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr12:49931200-49932800	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:49931200-49932800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:49931200-49933400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr12:49931200-49933400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:49931200-49935000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
36	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
39	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
42	chr12:49931400-49931600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr12:49931400-49931600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
46	chr12:49931400-49931600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:49931400-49931600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:49931400-49931600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
50	chr12:49931400-49931600	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links